It's an oft-repeated maxim that one of the reasons that Windows operating systems are plagued by so many viruses, worms, and security exploits is because they are so popular. Extrapolating on this, many have remarked that if Linux, MacOS, or other OSes become more popular, they will attract the attention of virus writers. That may be true, but the increased attention will not necessarily yield the same quantity of viruses and other exploits, says a Register article. Update: Rebuttal article.

Apart from the parts where it was agreeing that Windows' popularity is one of the main reasons it is so vulnerable (see "monoculture" comments),

Actually that is incorrect. The author does not blame Windows vulnerability on the fact that it's a monoculture. He's saying that viruses can do a lot more damage in a monoculure. There's quite a difference here - your interpretation of what the author is really saying is erroneous.

it was mainly listing ways in which Linux was less capable and hand-waving about how "not being root" would stop worms spreading and dramatically limit local system damage, which is just plain false.

"Not being root" does limit the spreading worm, but it doesn't help local system damage, as in a user's file. That still doesn't contradict the fact that "not being root" is safer: it prevents situation A and doesn't affect situation B either way, which is safer than not having an effection on either situation.

So in fact it appears that the author - who incidentally is a computer security specialist - is right on both these counts, and you aren't. Sorry.